Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients
Authors: Joann Diray-Arce, Slim Fourati, Naresh Doni Jayavelu, Ravi Patel, Cole Maguire, Ana C. Chang, Ravi Dandekar, Jingjing Qi, Brian H. Lee, Patrick van Zalm, Andrew Schroeder, Ernie Chen, Anna Konstorum, Anderson Brito, Jeremy P. Gygi, Alvin Kho, Jing Chen, Shrikant Pawar, Ana Silvia Gonzalez-Reiche, Annmarie Hoch, Carly E. Milliren, James A. Overton, Kerstin Westendorf, Charles B. Cairns, Nadine Rouphael, Steven E. Bosinger, Seunghee Kim-Schulze, Florian Krammer, Lindsey Rosen, Nathan D. Grubaugh, Harm van Bakel, Michael Wilson, Jayant Rajan, Hanno Steen, Walter Eckalbar, Chris Cotsapas, Charles R. Langelier, Ofer Levy, Matthew C. Altman, Holden Maecker, Ruth R. Montgomery, Elias K. Haddad, Rafick P. Sekaly, Denise Esserman, Al Ozonoff, Patrice M. Becker, Alison D. Augustine, Leying Guan, Bjoern Peters, Steven H. Kleinstein, James Abraham, Michael Adkisson, Marisa Albert, Luz Torres Altamirano, Bonny Alvarenga, Matthew L. Anderson, Evan J. Anderson, Azlann Arnett, Hiromitsu Asashima, Mark A. Atkinson, Lindsey R. Baden, Brenda Barton, Katherine Beach, Elizabeth Beagle, Patrice M. Becker, Matthew R. Bell, Mariana Bernui, Christian Bime, Arun Kumar Boddapati, J. Leland Booth, Brittney Borresen, Scott C. Brakenridge, Laurel Bristow, Robert Bryant, Carolyn S. Calfee, Juan Manuel Carreño, Sidney Carrillo, Suzanna Chak, Iris Chang, Jennifer Connors, Michelle Conway, David B. Corry, David Cowan, Brett Croen, Charles S. Dela Cruz, Gina Cusimano, Lily Eaker, Carolyn Edwards, Lauren I.R. Ehrlich, David Elashoff, Heidi Erickson, David J. Erle, Shelli Farhadian, Keith Farrugia, Benoit Fatou, Andrea Fernandes, Ana Fernandez-Sesma, Gabriela K. Fragiadakis, Sara Furukawa, Janelle N. Geltman, Rajani Ghale, Maria Carolina Bermúdez González, I. Michael Goonewardene, Estella Sanchez Guerrero, Faheem W. Guirgis, David A. Hafler, Sydney Hamilton, Paul Harris, Arash Nemati Hayati, Carolyn M. Hendrickson, Nelson I. Agudelo Higuita, Thomas Hodder, Steven M. Holland, Catherine L. Hough, Christopher Huerta, Kerin C. Hurley, Scott R. Hutton, Akiko Iwasaki, Alejandra Jauregui, Meenakshi Jha, Brandi Johnson, David Joyner, Kirsten N. Kangelaris, Geoffrey Kelly, Zain Khalil, Zenab Khan, Farrah Kheradmand, James N. Kim, Hiroki Kimura, Albert I. Ko, Bernard Kohr, Monica Kraft, Matthew Krummel, Michele A. Kutzler, Jessica Lasky-Su, Serena Lee, Deanna Lee, Michael Leipold, Claudia Lentucci, Carolyn Leroux, Edward Lin, Shanshan Liu, Christina Love, Zhengchun Lu, Lenka Maliskova, Brittany Roth Manning, Monali Manohar, Mark Martens, Grace A. McComsey, Kerry McEnaney, Renee McLin, Esther Melamed, Nataliya Melnyk, Kevin Mendez, William B. Messer, Jordan P. Metcalf, Gregory Michelotti, Eran Mick, Subhasis Mohanty, Jarrod Mosier, Lubbertus C.F. Mulder, Maimouna Murphy, Kari R.C. Nadeau, Ebony Nelson, Allison Nelson, Viet Nguyen, Jordan Oberhaus, Bernadine Panganiban, Kathryn L. Pellegrini, Harry C. Pickering, Debra L. Powell, Scott Presnell, Bali Pulendran, Adeeb H. Rahman, Ahmad Sadeed Rashid, Ariel Raskin, Elaine F. Reed, Susan Pereira Ribeiro, Adreanne M. Rivera, Jacob E. Rogers, Angela Rogers, Brandon Rogowski, Rebecca Rooks, Yael Rosenberg-Hasson, Jessica Rothman, Justin F. Rousseau, Ramin Salehi-Rad, Mehmet Saluvan, Hady Samaha, Joanna Schaenman, Ron Schunk, Nicholas C. Semenza, Subha Sen, Jonathan Sevransky, Vicki Seyfert-Margolis, Tanzia Shaheen, Albert C. Shaw, Scott Sieg, Sarah A.R. Siegel, Natalia Sigal, Nadia Siles, Brent Simmons, Viviana Simon, Gagandeep Singh, Lauren Sinko, Cecilia M. Smith, Kinga K. Smolen, Li-Zhen Song, Komal Srivastava, Peter Sullivan, Caitlin Syphurs, Johnstone Tcheou, George P. Tegos, Greg K. Tharp, Alexandra Tong, Alexandra Tsitsiklis, Ricardo F. Ungaro, Tatyana Vaysman, Arthur Viode, Randi Vita, Xiaomei Wang, Alyssa Ward, Dawn C. Ward, Andrew Willmore, Kyra Woloszczuk, Kari Wong, Prescott G. Woodruff, Leqi Xu, Simon van Haren, Adriana van de Guchte, Yujiao Zhao
Journal: Cell Reports Medicine (2023)

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1–3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.